Cuminc | R Documentation |

This function computes nonparametric cumulative incidence functions and associated standard errors for each value of a group variable.

```
Cuminc(time, status, data, group, na.status = c("remove", "extra"), ...)
```

`time` |
Either 1) a numeric vector containing the failure times or 2) a string containing the column name indicating these failure times |

`status` |
Either 1) a numeric, factor or character vector containing the failure codes or 2) a string containing the column name indicating these failure codes |

`data` |
When appropriate, a data frame containing |

`group` |
Optionally, name of column in data indicating a grouping
variable; cumulative incidence functions are calculated for each value or
level of |

`na.status` |
One of |

`...` |
Allows extra arguments for future extensions, but for now just
used for backwards compatibility (e.g. allowing use of defunct |

The estimated cumulative incidences are as described in Putter, Fiocco & Geskus (2007); the standard errors are the square roots of the Greenwood variance estimators, see eg. Andersen, Borgan, Gill & Keiding (1993), de Wreede, Fiocco & Putter (2009), and they correspond to the variances in eg. Marubini & Valsecchi (1995). In case of no censoring, the estimated cumulative incidences and variances reduce to simple binomial frequencies and their variances.

An object of class `"Cuminc"`

, which is a data frame containing
the estimated failure-free probabilities and cumulative incidences and their
standard errors. The names of the dataframe are `time`

, `Surv`

,
`seSurv`

, and `cuminc`

and `secuminc`

followed by the values
or levels of the `failcodes`

. If `group`

was specified, a
`group`

variable is included with the same name and values/levels as
the original grouping variable, and with estimated cumulative incidences
(SE) for each value/level of `group`

.

Cuminc is now simply a wrapper around survfit of the survival package with
type=`"mstate"`

, only maintained for backward compatibility. The
survfit object is kept as attribute (`attr("survfit")`

), and the print,
plot and summary functions are simply print, plot and summary applied to the
survfit object. Subsetting the `"Cuminc"`

object results in subsetting
the data frame, not in subsetting the survfit object.

Hein Putter H.Putter@lumc.nl

Andersen PK, Borgan O, Gill RD, Keiding N (1993).
*Statistical Models Based on Counting Processes*. Springer, New York.

Marubini E, Valsecchi MG (1995). *Analysing Survival Data from Clinical
Trials and Observational Studies*. Wiley, New York.

Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing
risks and multi-state models. *Statistics in Medicine* **26**,
2389–2430.

de Wreede L, Fiocco M, Putter H (2009). The mstate package for estimation and prediction in non- and semi-parametric multi-state models. Submitted.

```
### These data were used in Putter, Fiocco & Geskus (2007)
data(aidssi)
ci <- Cuminc(time=aidssi$time, status=aidssi$status)
head(ci); tail(ci)
ci <- Cuminc(time="time", status="status", data=aidssi, group="ccr5")
head(ci); tail(ci)
### Some fake data
fake <- data.frame(surv=c(seq(2,10,by=2),seq(1,13,by=3),seq(1,9,by=2),seq(1,13,by=3)),
stat=rep(0:3,5),Tstage=c(1:4,rep(1:4,rep(4,4))))
fake$stat[fake$stat==0 & fake$Tstage==2] <- 3
fake$stat[fake$stat==3 & fake$Tstage==1] <- 2
fake
Cuminc(time="surv", status="stat", data=fake)
# If we remove all entries with status=0,
# we should get binomial sample probabilities and corresponding SEs
fake0 <- fake[fake$stat!=0,]
Cuminc(time="surv", status="stat", data=fake0)
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.